poli.core.proteins.foldx_black_box.FoldxBlackBox

poli.core.proteins.foldx_black_box.FoldxBlackBox#

class poli.core.proteins.foldx_black_box.FoldxBlackBox(info: Optional[BlackBoxInformation] = None, batch_size: Optional[int] = None, parallelize: bool = False, num_workers: Optional[int] = None, evaluation_budget: int = inf, wildtype_pdb_path: Optional[Union[Path, List[Path]]] = None, alphabet: Optional[List[str]] = None, experiment_id: Optional[str] = None, tmp_folder: Optional[Path] = None, eager_repair: bool = False, verbose: bool = False)#

A class representing the FoldxBlackBox, which is used for simulating protein mutations using FoldX.

Parameters

info (ProblemSetupInformation, required) – The problem setup information object. (default: None)
batch_size (int, optional) – The batch size for parallelization. (default: None)
parallelize (bool, optional) – Flag indicating whether to parallelize the simulations. (default: False)
num_workers (int, optional) – The number of workers for parallelization. (default: None)
wildtype_pdb_path (Union[Path, List[Path]], required) – The path(s) to the wildtype PDB file(s). (default: None)
alphabet (List[str], optional) – The list of allowed amino acids. (default: None)
experiment_id (str, optional) – The experiment ID. (default: None)
tmp_folder (Path, optional) – The temporary folder path. (default: None)
eager_repair (bool, optional) – Flag indicating whether to eagerly repair the PDB files. (default: False)
verbose (bool, optional) – Flag indicating whether we print the output from FoldX. (default: False)

experiment_id#

The experiment ID.

Type: str

tmp_folder#

The temporary folder path.

Type: Path

wildtype_pdb_paths#

The list of repaired wildtype PDB file paths.

Type: List[Path]

wildtype_residues#

The list of wildtype residues for each PDB file.

Type: List[List[Residue]]

wildtype_amino_acids#

The list of wildtype amino acids for each PDB file.

Type: List[List[str]]

wildtype_residue_strings#

The list of wildtype residue strings for each PDB file.

Type: List[str]

create_working_directory() → Path:#: Creates and returns the working directory path for the black box.

__init__(info: Optional[BlackBoxInformation] = None, batch_size: Optional[int] = None, parallelize: bool = False, num_workers: Optional[int] = None, evaluation_budget: int = inf, wildtype_pdb_path: Optional[Union[Path, List[Path]]] = None, alphabet: Optional[List[str]] = None, experiment_id: Optional[str] = None, tmp_folder: Optional[Path] = None, eager_repair: bool = False, verbose: bool = False)#

Initialize the FoldxBlackBox.

Parameters

info (ProblemSetupInformation, optional) – The problem setup information object. (default: None)
batch_size (int, optional) – The batch size for parallelization. (default: None)
parallelize (bool, optional) – Flag indicating whether to parallelize the simulations. (default: False)
num_workers (int, optional) – The number of workers for parallelization. (default: None)
evaluation_budget (int, optional) – The evaluation budget. (default: float(‘inf’))
wildtype_pdb_path (Union[Path, List[Path]], optional) – The path(s) to the wildtype PDB file(s). (default: None)
alphabet (List[str], optional) – The list of allowed amino acids. (default: None)
experiment_id (str, optional) – The experiment ID. (default: None)
tmp_folder (Path, optional) – The temporary folder path. (default: None)
eager_repair (bool, optional) – Flag indicating whether to eagerly repair the PDB files. (default: False)
verbose (bool, optional) – Flag indicating whether we print the output from FoldX. (default: False)

Methods

`__init__`([info, batch_size, parallelize, ...])	Initialize the FoldxBlackBox.
`create_working_directory`()	Create and return the working directory path for the black box.
`reset_evaluation_budget`()	Resets the evaluation budget by setting the number of evaluations made to 0.
`set_observer`(observer)	Set the observer object for recording observations during evaluation.
`terminate`()	Terminate the black box optimization problem.